28 December 2014
As as you already mentioned that Rs. 10,00,000 is wrongly included in turnover and consequently assessee has paid excess tax as required to legally pay.
If case comes under scrutiny and you have sufficient records for that purpose you can claim refund by making ratification under section 154
29 December 2014
U/s.154(2) on application made by the assessee, the income tax authority may make the rectification. So you need not wait until the case taken up for scrutiny. You can save your money through this process.